It is 1936, South America, Peru. Indiana Jones is getting through the jungles with two hired men, he is looking for the golden idol. When he finds it and successfully leaves the temple with numerous traps, a group of locals meets him outside. They are headed by Rene Belloq, his opponent. Indiana is forced to give him the idol and manages to escape.
When Indiana is back to San Francisco, two Army Intelligence agents come to him with information that the Nazis are looking for his mentor Abner Ravenwood who was an expert in Egyptian archaeology and owned an artifact called the Staff of Ra. In the letter overtaken from the Nazis the city of Tanis is mentioned, so Indiana assumes that the Nazis are searching for the Ark of the Covenant – the most precious artifact in the world. It is believed to have power of God, and the one who would possess it would be invincible.
The agents sent Indiana to find the Ark before the Nazis. On his way to Cairo Indiana visits Ravenwood’s daughter Marion in Nepal. They used to be lovers, and she is very mad at him and does not want to help and give him the medallion, but when the Nazis rush into her tavern and burn everything there she goes with Indiana to Egypt.
There in Egypt they find out that the Nazis are digging for the Well of Souls, but it is the wrong place. With the help of the medallion Indiana finds the right place, and finds there the Ark. But at that moment the Nazis with Rene Belloq come and take away the Ark leaving Indiana dying in the temple full of snakes. But Indiana successfully finds the way out and tries to catch the truck with the Ark in it. He manages to do it and even is already on the board of the ship to London, but the Nazis find him there and take the Ark away.
Rene Belloq offers the Nazis captain to open the Ark and to see whether the tables are in it. The captain agrees because he is afraid to fail the mission and bring Hitler an empty Ark. When they open the Ark the souls of dead are released from it and take everyone present in it. Only Indiana and Marion stay alive, because they keep their eyes closed.
When back in Washington, Indiana is informed that the Ark is in a safe place. The next scene reveals a wooden box being stored in a big department with many other wooden boxes.